You can autoclave Milli-Q water in autoclavable glass flasks if you want to, but many bioforum users afaik use Milli-Q directly. If your system is cleaned regulary and you don't contaminate it while out of the fiter, you can hardly get PCR contaminants there.

But for checking just do a negative control (PCR setup for some well working DNA assay mix with primers with water instead of template), and do it with every other assay you run. I don't know what is your custom, but usually we run PCR on agarose gel, not acrylamide, but that probably doesn't matter as much.

But that can't tell you if you have a nuclease contamination in your water. You would know that, if your DNA will be degraded, instead of single band on 0.7% agarose gel, you will see a smear and your PCR would be failing. It can't also tell you about PCR inhibitors contamination, that would also make your test PCR fail.

But again, that is unlikely to hapen with Milli-Q water.

So make some PCR with positive template and without template and if you got a product in positive sample, and no product in negative, you are probably OK.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.

But I'd avoid autoclaving the water since this won't remove possible contaminants (i.e. DNA) but might add new dirt.

One must presume that long and short arguments contribute to the same end. - Epicurus...except casandra's that did belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.

hobglobin: I would say incorrect handling during autoclaving can add new dirt (or dirty/rusty jars used for plastics for example). Or if the autoclave is really nasty. Anyway it's better to put milliq water into clean glass flask, that has been autoclaved before use. While the water is extra pure in the MIllipore machine, the containers you put it in, often are not. It's a matter of decision to autoclave it after, since of course autoclave won't get rid of DNA or even ions, but may get rid of potential "living" contaminats that you introduce to the water while handling it in the open air.

Our country has a serious deficiency in lighthouses. I assume the main reason is that we have no sea.